A knowledge-based structure-discriminating function that requires only main-chain atom coordinates

BMC Structural Biology

Table 1 Parameters and their values for tuning the function.

scan	component	parameter	initial value	scanned values	selected value
1	DIST	b	12.0	9.0, 10.0, 11.0, 12.0, 13.0, 14.0, 15.0	12.0
		c	0.627	0.525, 0.550, 0.575, 0.603, 0.631, 0.661, 0.692	0.661
2	DIST	sequence separation limit	5	2, 3, 4, 5, 6, 7, 8	5
3	DABG	range of the bin averaging
		distance	1	0, 1, 2	0
		α angle	0	0, 1	1
		β angle	0	0, 1	0
		γ angle	2	0, 1, 2	1
4	DABG	sequence separation limit	5	2, 3, 4, 5, 6, 7, 8	5
5	DIST, DABG	sequence separation limit of evaluation	3	1, 2, 3, 4, 5, 6, 7, 8, 9, 10	3
6	DIST	0 count penalty	8.0	0.0, 2.0, 4.0, 6.0, 8.0, 10.0, 12.0, 14.0, 16.0	8.0
7	DABG	0 count penalty	2.0	0.0, 1.0, 2.0, 3.0, 4.0, 5.0	2.0
8	SURR	radius range	15.0	9.0, 12.0, 15.0, 18.0	15.0
9	SURR	0 count penalty	0.0	0.0, 1.0, 2.0, 3.0, 4.0, 5.0, 6.0, 7.0	0.0
10	HBND	0 count penalty	2.0	0.0, 1.0, 2.0, 3.0, 4.0, 5.0, 6.0, 7.0	2.0
11	PPDA	0 count penalty	12.0	0.0, 2.0, 4.0, 6.0, 8.0, 10.0, 12.0, 14.0, 16.0	12.0
12	OMDA	0 count penalty	6.0	0.0, 2.0, 4.0, 6.0, 8.0, 10.0, 12.0, 14.0, 16.0	0.0

Short descriptions of scanned parameters of the components are shown in the order of scanning during the tuning process. The b and c of scan 1 are the constants for calculating N_exp(d). Sequence separation limit of scan 2 and 4 are the lower limit of separation between i^th and j^th residues that was incorporated into the respective databases. The four parameters of scan 3 are the range for averaging among adjacent database bins. The sequence separation limit of evaluation of scan 5 is the lower limit of separation applied for evaluation, not for database construction. The 0 count penalties of scan 6, 7, 9, 10, 11 and 12 are the energy penalty value when no count was recorded in the bin of the compiled database. The radius range of scan 8 is the radius of the sphere for SURR component calculation. Details of the respective parameters are in Methods. The values determined by initial scanning before tuning, the list of scanned values during tuning, and the selected values with better C_αRMSD are shown. Multiple parameters in a single scan indicate the scanning of all combinations among the listed values.

ISSN: 1472-6807